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Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity

Author

Listed:
  • Jason Saba

    (University of Wisconsin–Madison
    University of Wisconsin–Madison)

  • Katia Flores

    (University of Chicago
    University of Chicago)

  • Bailey Marshall

    (University of Wisconsin–Madison
    University of Wisconsin–Madison)

  • Michael D. Engstrom

    (University of Wisconsin–Madison)

  • Yikai Peng

    (University of Wisconsin–Madison)

  • Atharv S. Garje

    (University of Wisconsin–Madison
    University of Wisconsin–Madison)

  • Laurie E. Comstock

    (University of Chicago
    University of Chicago)

  • Robert Landick

    (University of Wisconsin–Madison
    University of Wisconsin–Madison)

Abstract

The genomes of human gut bacteria in the genus Bacteroides include numerous operons for biosynthesis of diverse capsular polysaccharides (CPSs). The first two genes of each CPS operon encode a locus-specific paralog of transcription elongation factor NusG (called UpxY), which enhances transcript elongation, and a UpxZ protein that inhibits noncognate UpxYs. This process, together with promoter inversions, ensures that a single CPS operon is transcribed in most cells. Here, we use in-vivo nascent-RNA sequencing and promoter-less in-vitro transcription (PIVoT) to show that UpxY recognizes a paused RNA polymerase via sequences in both the exposed non-template DNA and the upstream duplex DNA. UpxY association is aided by ‘pause-then-escape’ nascent RNA hairpins. UpxZ binds non-cognate UpxYs to directly inhibit UpxY association. This UpxY-UpxZ hierarchical regulatory program allows Bacteroides to generate subpopulations of cells producing diverse CPSs for optimal fitness.

Suggested Citation

  • Jason Saba & Katia Flores & Bailey Marshall & Michael D. Engstrom & Yikai Peng & Atharv S. Garje & Laurie E. Comstock & Robert Landick, 2024. "Bacteroides expand the functional versatility of a conserved transcription factor and transcribed DNA to program capsule diversity," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-55215-9
    DOI: 10.1038/s41467-024-55215-9
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